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21 changes: 13 additions & 8 deletions content/en/docs/Concepts/neuron-counts.md
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Expand Up @@ -43,7 +43,7 @@ These are the datasets Virtual Fly Brain holds. Each row is one animal.
|---|---|---|---|---|
| **FlyWire** (FAFB) | **139,255** | Whole brain, both optic lobes included. VNC excluded | Adult **female**, ssTEM | Dorkenwald et al. 2024, *Nature* 634:124–138 · PMID 39358518 · doi:10.1038/s41586-024-07558-y |
| **Male CNS** v1.0 | **~166,700** | **Whole CNS** — central brain + optic lobes + VNC, intact neck connective | Adult **male**, eFIB-SEM | Berg et al. 2026, *Cell* 189(18):5504–5526.e15 · PMID 42691995 · doi:10.1016/j.cell.2026.08.015 |
| **BANC** v626 | **155,916** | Brain + VNC in one animal. **Lamina and ocellar ganglion absent** (~9,390 lamina neurons missing) | Adult **female**, ssTEM (GridTape) | Bates et al. 2026, *Nature* · PMID 42259917 · doi:10.1038/s41586-026-10735-w |
| **BANC** v888 | **155,916** | Brain + VNC in one animal. **Lamina and ocellar ganglion absent** (~9,390 lamina neurons missing) | Adult **female**, ssTEM (GridTape) | Bates et al. 2026, *Nature* · PMID 42259917 · doi:10.1038/s41586-026-10735-w |
| **Optic lobe** v1.0.1 | **~53,000** (732 cell types) | **Right optic lobe only.** Lamina incomplete; central brain not proofread | Adult **male**, FIB-SEM | Nern et al. 2025, *Nature* 641:1225–1237 · PMID 40140576 |
| **MANC** v1.2.1 | **~23,000** ("roughly 23 thousand") | **Ventral nerve cord only**, plus the neck connective | 5-day **male**, FIB-SEM | Takemura et al. 2024, *eLife* 13:RP97769 · **reviewed preprint, no version of record, no PMID** |
| **Hemibrain** v1.2.1 | **~25,000** | **A portion of the central brain** — see §2 | 5-day **female** Canton S, FIB-SEM | Scheffer et al. 2020, *eLife* 9:e57443 · PMID 32880371 |
Expand All @@ -69,12 +69,13 @@ factor that could be corrected for:
| Hemibrain v1.2.1 | 69,578 | ~25,000 | 2.78 |
| Optic lobe v1.0.1 | 60,002 | ~53,000 | 1.13 |
| Male CNS v1.0 | 340,230 | ~166,700 | 2.04 |
| **BANC v626** | **143,806** | **155,916** | **0.92** |
| **BANC v888** | **186,392** | **155,916** | **1.20** |

The ratio ranges from 0.92 to 2.78 — and BANC has *fewer* images than the paper reports neurons, so
the error does not even run in a consistent direction. Neurons are aligned to multiple template brains
(one neuron can appear as several images), while other neurons in a release may have no aligned image
at all. **An image count is a count of images.**
The ratio ranges from 1.13 to 2.78 — a factor of almost 2.5 between datasets, so there is no constant
to correct by. It does not even run in a consistent direction: for BANC v626, the release VFB held
before v888, there were *fewer* images (143,806) than the paper reports neurons. Neurons are aligned to
multiple template brains (one neuron can appear as several images), while other neurons in a release
may have no aligned image at all. **An image count is a count of images.**

One practical note for anyone querying this: `get_term_info` reports `count: -1` for `DatasetImages`,
which is the unavailable sentinel and not zero. The real totals only come back from `run_query`.
Expand Down Expand Up @@ -168,8 +169,12 @@ This is the single most useful thing to know when quoting any connectome figure.
- **Shiu et al.'s model, built on FlyWire materialisation v630, used 127,400 neurons** — the same brain,
a different materialisation, ~12,000 fewer neurons.
- **BANC's preprint reports 142,719 proofread neurons at v821; the *Nature* version reports 155,916**
proofread plus roughly-proofread. The paper's analyses are performed on v626 — the version VFB holds
— but no neuron total is ever published for v626 specifically.
— 150,841 backbone proofread plus 5,075 roughly proofread — at v888, the release VFB holds (a
snapshot of 17 April 2026). Between the preprint and v888, 62,773 proofread and roughly proofread
neurons were updated, 42,270 of them new. The paper also notes that BANC's published metadata marks
some neurons proofread after the snapshot, so a count taken from the live tables drifts: in October
2026, `banc_888_meta` gave 155,858 proofread and roughly proofread neurons, excluding glia, trachea
and non-neurons.
- **The optic lobe cell-type count went from 727 to 732** between preprint (v1.0) and version of record
(v1.1). VFB holds v1.0.1, which neither citation documents.
- **MANC's companion papers disagree with each other** by a handful of neurons per class, and Marin et
Expand Down
2 changes: 1 addition & 1 deletion content/en/docs/Data/EM/_index.md
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Expand Up @@ -21,7 +21,7 @@ The table below summarises EM datasets that have been integrated into VFB, inclu

| Dataset | VFB symbol | Version in VFB | Stage | Anatomy | Reconstruction | Resource(s) | Original Publication |
|---|---|---|---|---|---|---|---|
| BANC | `BANC` | v626 | Adult | Full CNS (adult female) | Dense | [Codex](https://codex.flywire.ai/?dataset=banc&data_version=626) | [Bates et al. (2025)](https://doi.org/10.1101/2025.07.31.667571), published as [Bates et al. (2026)](https://doi.org/10.1038/s41586-026-10735-w) |
| BANC | `BANC` | v888 | Adult | Full CNS (adult female) | Dense | [Codex](https://codex.flywire.ai/?dataset=banc&data_version=888) | [Bates et al. (2025)](https://doi.org/10.1101/2025.07.31.667571), published as [Bates et al. (2026)](https://doi.org/10.1038/s41586-026-10735-w) |
| male-CNS | `mc` | v1.0 | Adult | Full CNS (adult male) | Dense | [NeuPrint](https://neuprint.janelia.org/?dataset=male-cns%3Av1.0&qt=findneurons); [Codex](https://codex.flywire.ai/) | [Berg et al. (2025)](https://doi.org/10.1101/2025.10.09.680999), published as [Berg et al. (2026)](https://doi.org/10.1016/j.cell.2026.08.015) |
| Optic-lobe | `ol` | v1.0.1 | Adult | Optic lobe (adult male) | Dense | [NeuPrint](https://neuprint.janelia.org/?dataset=optic-lobe%3Av1.0.1&qt=findneurons); [Codex](https://codex.flywire.ai/) | [Nern et al. (2025)](https://doi.org/10.1038/s41586-025-08746-0) |
| FAFB (FlyWire) | `fw` | v783 | Adult | Full brain (adult female) | Dense | [Codex](https://codex.flywire.ai/?data_version=783) | [Dorkenwald et al. (2024)](https://doi.org/10.1038/s41586-024-07558-y); [Schlegel et al. (2024)](https://doi.org/10.1038/s41586-024-07686-5) |
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2 changes: 1 addition & 1 deletion content/en/docs/Data/connectivity.md
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Expand Up @@ -42,7 +42,7 @@ from curation, so they carry no synapse counts and cover far fewer entities. The

| Dataset | VFB symbol | Coverage |
|---|---|---|
| BANC v626 | `BANC` | Full CNS, adult female |
| BANC v888 | `BANC` | Full CNS, adult female |
| FlyWire v783 (FAFB) | `fw` | Full brain, adult female |
| male-CNS v1.0 | `mc` | Full CNS, adult male |
| MANC v1.2.1 | `mv` | Full VNC, adult male |
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2 changes: 1 addition & 1 deletion content/en/docs/Data/stages.md
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Expand Up @@ -337,7 +337,7 @@ whole animal rather than the nervous system alone.

| Dataset | Short form |
|---|---|
| [Full CNS EM connectome, dense reconstruction (adult female)](https://virtualflybrain.org/reports/Bates2025) | `Bates2025` |
| [Full CNS EM connectome, dense reconstruction (adult female)](https://virtualflybrain.org/reports/Bates2026) | `Bates2026` |
| [Full CNS EM connectome, dense reconstruction (adult male)](https://virtualflybrain.org/reports/Berg2025a) | `Berg2025a` |
| [Neurons involved in courtship and song (Lillvis2018)](https://virtualflybrain.org/reports/Lillvis2018) | `Lillvis2018` |
| [Single-nucleus RNA-seq on cells from 30-days old female flies](https://flybase.org/reports/FBlc0006424) | `FBlc0006424` |
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